LOCUS       NM_006898               2449 bp    mRNA    linear   PRI 09-JUN-2024
DEFINITION  Homo sapiens homeobox D3 (HOXD3), mRNA.
ACCESSION   NM_006898 XM_005246513
VERSION     NM_006898.5
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2449)
  AUTHORS   Wang,L., Wang,X., Sun,H., Wang,W. and Cao,L.
  TITLE     A pan-cancer analysis of the role of HOXD1, HOXD3, and HOXD4 and
            validation in renal cell carcinoma
  JOURNAL   Aging (Albany NY) 15 (19), 10746-10766 (2023)
   PUBMED   37827698
  REMARK    GeneRIF: A pan-cancer analysis of the role of HOXD1, HOXD3, and
            HOXD4 and validation in renal cell carcinoma.
REFERENCE   2  (bases 1 to 2449)
  AUTHORS   Wang,H., Zhou,Z., Liu,Y., Wang,P., Chen,L., Qi,S., Xie,J. and
            Tang,J.
  TITLE     Identification and validation of HOXD3 and UNC5C as molecular
            signatures in keloid based on weighted gene co-expression network
            analysis
  JOURNAL   Genomics 114 (4), 110403 (2022)
   PUBMED   35709926
  REMARK    GeneRIF: Identification and validation of HOXD3 and UNC5C as
            molecular signatures in keloid based on weighted gene co-expression
            network analysis.
REFERENCE   3  (bases 1 to 2449)
  AUTHORS   Cui,Y., Lv,C., Wen,Y., Zhao,D., Yang,Y., Qiu,H. and Wang,C.
  TITLE     HOXD3 Up-regulating KDM5C Promotes Malignant Progression of Diffuse
            Large B-Cell Lymphoma by Decreasing p53 Expression
  JOURNAL   Balkan Med J 39 (1), 30-38 (2022)
   PUBMED   34928233
  REMARK    GeneRIF: HOXD3 Up-regulating KDM5C Promotes Malignant Progression
            of Diffuse Large B-Cell Lymphoma by Decreasing p53 Expression
REFERENCE   4  (bases 1 to 2449)
  AUTHORS   Wang,L., Gao,Y., Zhao,X., Guo,C., Wang,X., Yang,Y., Han,C.,
            Zhao,L., Qin,Y., Liu,L., Huang,C. and Wang,W.
  TITLE     HOXD3 was negatively regulated by YY1 recruiting HDAC1 to suppress
            progression of hepatocellular carcinoma cells via ITGA2 pathway
  JOURNAL   Cell Prolif 53 (8), e12835 (2020)
   PUBMED   32557953
  REMARK    GeneRIF: HOXD3 was negatively regulated by YY1 recruiting HDAC1 to
            suppress progression of hepatocellular carcinoma cells via ITGA2
            pathway.
REFERENCE   5  (bases 1 to 2449)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   6  (bases 1 to 2449)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
REFERENCE   7  (bases 1 to 2449)
  AUTHORS   Taniguchi,Y., Fujii,A. and Moriuchi,T.
  TITLE     Cloning and sequencing of the human homeobox gene HOX4A
  JOURNAL   Biochim Biophys Acta 1132 (3), 332-334 (1992)
   PUBMED   1358204
REFERENCE   8  (bases 1 to 2449)
  AUTHORS   McAlpine,P.J. and Shows,T.B.
  TITLE     Nomenclature for human homeobox genes
  JOURNAL   Genomics 7 (3), 460 (1990)
   PUBMED   1973146
REFERENCE   9  (bases 1 to 2449)
  AUTHORS   Acampora,D., D'Esposito,M., Faiella,A., Pannese,M., Migliaccio,E.,
            Morelli,F., Stornaiuolo,A., Nigro,V., Simeone,A. and Boncinelli,E.
  TITLE     The human HOX gene family
  JOURNAL   Nucleic Acids Res 17 (24), 10385-10402 (1989)
   PUBMED   2574852
REFERENCE   10 (bases 1 to 2449)
  AUTHORS   Boncinelli,E., Acampora,D., Pannese,M., D'Esposito,M., Somma,R.,
            Gaudino,G., Stornaiuolo,A., Cafiero,M., Faiella,A. and Simeone,A.
  TITLE     Organization of human class I homeobox genes
  JOURNAL   Genome 31 (2), 745-756 (1989)
   PUBMED   2576652
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC009336.13.
            
            On or before Jul 2, 2019 this sequence version replaced
            XM_005246513.5, NM_006898.4.
            
            Summary: This gene belongs to the homeobox family of genes. The
            homeobox genes encode a highly conserved family of transcription
            factors that play an important role in morphogenesis in all
            multicellular organisms. Mammals possess four similar homeobox gene
            clusters, HOXA, HOXB, HOXC and HOXD, located on different
            chromosomes, consisting of 9 to 11 genes arranged in tandem. This
            gene is one of several homeobox HOXD genes located at 2q31-2q37
            chromosome regions. Deletions that removed the entire HOXD gene
            cluster or 5' end of this cluster have been associated with severe
            limb and genital abnormalities. The protein encoded by this gene
            may play a role in the regulation of cell adhesion processes.
            [provided by RefSeq, Jul 2008].
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: ERR4352443.714321.1,
                                           SRR14038193.2368559.1 [ECO:0000332]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000683222.1/ ENSP00000507129.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-146               AC009336.13        141296-141441
            147-242             AC009336.13        148062-148157
            243-867             AC009336.13        153020-153644
            868-2449            AC009336.13        155506-157087
FEATURES             Location/Qualifiers
     source          1..2449
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q31.1"
     gene            1..2449
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
                     /note="homeobox D3"
                     /db_xref="GeneID:3232"
                     /db_xref="HGNC:HGNC:5137"
                     /db_xref="MIM:142980"
     exon            1..146
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
                     /inference="alignment:Splign:2.1.0"
     exon            147..242
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
                     /inference="alignment:Splign:2.1.0"
     exon            243..867
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
                     /inference="alignment:Splign:2.1.0"
     CDS             327..1625
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
                     /note="homeo box D3; Hox-4.1, mouse, homolog of; homeobox
                     protein Hox-4A"
                     /codon_start=1
                     /product="homeobox protein Hox-D3"
                     /protein_id="NP_008829.3"
                     /db_xref="CCDS:CCDS2270.1"
                     /db_xref="GeneID:3232"
                     /db_xref="HGNC:HGNC:5137"
                     /db_xref="MIM:142980"
                     /translation="MLFEQGQQALELPECTMQKAAYYENPGLFGGYGYSKTTDTYGYS
                     TPHQPYPPPAAASSLDTDYPGSACSIQSSAPLRAPAHKGAELNGSCMRPGTGNSQGGG
                     GGSQPPGLNSEQQPPQPPPPPPTLPPSSPTNPGGGVPAKKPKGGPNASSSSATISKQI
                     FPWMKESRQNSKQKNSCATAGESCEDKSPPGPASKRVRTAYTSAQLVELEKEFHFNRY
                     LCRPRRVEMANLLNLTERQIKIWFQNRRMKYKKDQKAKGILHSPASQSPERSPPLGGA
                     AGHVAYSGQLPPVPGLAYDAPSPPAFAKSQPNMYGLAAYTAPLSSCLPQQKRYAAPEF
                     EPHPMASNGGGFASANLQGSPVYVGGNFVESMAPASGPVFNLGHLSHPSSASVDYSCA
                     AQIPGNHHHGPCDPHPTYTDLSAHHSSQGRLPEAPKLTHL"
     exon            868..2449
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2417..2422
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
                     /note="hexamer: AACAAA"
     regulatory      2430..2435
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
                     /note="hexamer: AATAAA"
     polyA_site      2439
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
     polyA_site      2449
                     /gene="HOXD3"
                     /gene_synonym="Hox-4.1; HOX1D; HOX4; HOX4A"
                     /note="major polyA site"
ORIGIN      
        1 ggagtcgtca ttaatctgcc acgcaaaggg ctctctccga cttggaaagt gcagggatcc
       61 caagaatatc acccgtccag gggggccgcg cggtgccccc ggccctccac ccccggcccc
      121 cggcgggcgc gggagcgcgg ccgcagattc gcctccacag atatcaaaag aaacctgaag
      181 agcctacaaa aaaaaaagag ataaagacaa aattcaagaa aacacacaca tacataattg
      241 tggtcacctg gagcctgggg gccggcccag ctctctcagg attcagcaga cattggaggt
      301 ggcagtgaag gatacagtgg tagtcaatgt tatttgagca gggtcagcag gccctggagc
      361 ttcctgagtg cacaatgcag aaggctgctt actatgaaaa cccaggactg tttggaggct
      421 atggctacag caaaactacg gacacttacg gctacagcac cccccaccag ccctacccac
      481 cccctgctgc tgccagctcc ctggacactg actatccagg ttctgcctgc tccatccaga
      541 gctctgcccc tctgagagcc ccagcccaca aaggagctga actcaatggc agctgcatgc
      601 ggccgggcac tgggaacagc cagggtgggg gtggtggcag ccagcctcct ggtctgaact
      661 cagagcagca gccaccacaa ccccctcctc caccaccgac cctgccccca tcttcaccca
      721 ccaatcctgg aggtggagtg cctgccaaga agcccaaagg tgggcccaat gcttctagct
      781 cctcagccac catcagcaag cagatcttcc cctggatgaa agagtctcga cagaactcca
      841 agcagaagaa cagctgtgcc actgcaggag agagctgcga ggacaagagc ccgccaggcc
      901 cagcatccaa gcgggtacgc acggcataca cgagcgcgca gctggtggaa ttggaaaagg
      961 aattccactt caaccgctac ttgtgccggc cgcgccgcgt ggagatggcc aacctgctga
     1021 atctcacgga acgccagatc aagatctggt tccagaaccg gcgcatgaag tacaagaagg
     1081 accagaaggc caagggcatc ctgcactcgc cggctagcca gtcccctgag cgcagcccac
     1141 cgctcggcgg cgccgctggc cacgtggcct actccggcca gctgccgcca gtgcccggcc
     1201 tggcctacga cgcgccctcg ccgcctgctt tcgccaaatc acagcccaat atgtacggcc
     1261 tggccgccta cacggcgcca ctcagcagct gcctgccaca acagaagcgc tacgcagcgc
     1321 cggagttcga gccccatccc atggcgagca acggcggcgg cttcgccagc gccaacttgc
     1381 agggcagccc ggtgtacgtg ggcggcaact tcgtcgagtc catggcgccc gcgtccgggc
     1441 ctgtcttcaa cctgggccac ctctcgcacc cgtcgtcggc cagcgtggac tacagttgcg
     1501 ccgcgcagat tccaggcaac caccaccatg gaccttgcga ccctcatccc acctacacag
     1561 atctctcggc ccaccactcg tctcagggac gactgccgga ggctcccaaa ctgacgcatc
     1621 tgtagcggcc gccgccagcc cgaactcgcg gcaaaattac ctctcttgct gtagtggtgg
     1681 ggtagagggt ggggcccgcg gggcagttcg ggaaccccct tccccgctct tgccctgccg
     1741 ccgcctcccg ggtctcaggc ctccagcggc ggaggcgcag gcgaccgggc ctcccctcca
     1801 tgggcgtcct ttgggtgact cgccataaat cagccgcaag gatccttccc tgtaaatttg
     1861 acagtgccac atactgcgga ccaagggact ccaatctggt aatggtgtcc caaaggtaag
     1921 tctgagaccc atcagcggcg cgccctgcag agggaccaga gcttggagag tcttgggcct
     1981 ggcccgcgtc tagcttagtt tcagagacct taatttatat tctccttcct gtgccgtaag
     2041 gattgcatcg gactaaacta tctgtattta ttatttgaag cgagtcattt cgttccctga
     2101 ttatttatcc ttgtctgaat gtatttatgt gtatatttgt agatttatcc agccgagctt
     2161 aggaattcgc ttccaggccg tgggggccac atttcacctc cttagtcccc ctggtctgaa
     2221 ctagttgaga gagtagtttt gaacagtcgt aaccgtggct ggtgtttgta gttgacataa
     2281 aggattaaga ccgcaaattg tccttcatgg gtagagtcag gaagcccggt ggcgtggcac
     2341 aacacacttt ggtcatttct caaaaaccac agtcctcacc acagtttatt gatttcaaat
     2401 tgtctggtac tattggaaca aatatttaga ataaaaaaat ttcccagtc
//
